# import external packages
import numpy as np
import json
from pathlib import Path

# import supporting pipeline classes (if any)
from utils.img_registration import image_registration, check_reg_prec
from tools.output_handling import load_dict_list_from_json, load_json_experiments_data, NumpyArrayEncoder

FoV_dict_list_BMY823_20230725_1_C = load_dict_list_from_json("/home/jocelyn.tourtellotte-umw/yeast_json_output/tracking_experiments/BMY823_BMY823_7_25_23_aqsettings1_batchC.json")

reg_dict_list_BMY823_20230725_1_C = []
for FoV_dict in FoV_dict_list_BMY823_20230725_1_C:
    reg_dict_list_BMY823_20230725_1_C.append(image_registration(FoV_dict))

<tifffile.TiffTag 5033 @135616> coercing invalid ASCII to bytes, due to UnicodeDecodeError('charmap', b'\x8d', 0, 1, 'character maps to <undefined>')
<tifffile.TiffTag 5031 @135592> coercing invalid ASCII to bytes, due to UnicodeDecodeError('charmap', b'\x81\n\x02', 0, 1, 'character maps to <undefined>')
<tifffile.TiffTag 5033 @135616> coercing invalid ASCII to bytes, due to UnicodeDecodeError('charmap', b'\x8d', 0, 1, 'character maps to <undefined>')
<tifffile.TiffTag 5033 @135616> coercing invalid ASCII to bytes, due to UnicodeDecodeError('charmap', b'\x8d', 0, 1, 'character maps to <undefined>')
<tifffile.TiffTag 5031 @135592> coercing invalid ASCII to bytes, due to UnicodeDecodeError('charmap', b'\x81\n\x02', 0, 1, 'character maps to <undefined>')
<tifffile.TiffTag 5033 @135616> coercing invalid ASCII to bytes, due to UnicodeDecodeError('charmap', b'\x8d', 0, 1, 'character maps to <undefined>')

---Image Registration---

translation = [ 4.085 -2.438]

rotation = -0.09503322835880113 

scale = 1.0010583594846616

<tifffile.TiffTag 5033 @135616> coercing invalid ASCII to bytes, due to UnicodeDecodeError('charmap', b'\x8d', 0, 1, 'character maps to <undefined>')
<tifffile.TiffTag 5031 @135592> coercing invalid ASCII to bytes, due to UnicodeDecodeError('charmap', b'\x81\n\x02', 0, 1, 'character maps to <undefined>')
<tifffile.TiffTag 5033 @135616> coercing invalid ASCII to bytes, due to UnicodeDecodeError('charmap', b'\x8d', 0, 1, 'character maps to <undefined>')

---Image Registration---

translation = [ 3.732 -2.513]

rotation = -0.18296085838895237 

scale = 1.000281121164851 


 registration difference vector: [np.float64(0.35299999999999976), np.float64(0.07499999999999973)]

<tifffile.TiffTag 5033 @135616> coercing invalid ASCII to bytes, due to UnicodeDecodeError('charmap', b'\x8d', 0, 1, 'character maps to <undefined>')
<tifffile.TiffTag 5031 @135592> coercing invalid ASCII to bytes, due to UnicodeDecodeError('charmap', b'\x81\n\x02', 0, 1, 'character maps to <undefined>')
<tifffile.TiffTag 5033 @135616> coercing invalid ASCII to bytes, due to UnicodeDecodeError('charmap', b'\x8d', 0, 1, 'character maps to <undefined>')

---Image Registration---

translation = [ 3.773 -2.449]

rotation = -0.16025335827720255 

scale = 0.9993170617522066

<tifffile.TiffTag 5033 @135616> coercing invalid ASCII to bytes, due to UnicodeDecodeError('charmap', b'\x8d', 0, 1, 'character maps to <undefined>')
<tifffile.TiffTag 5031 @135592> coercing invalid ASCII to bytes, due to UnicodeDecodeError('charmap', b'\x81\n\x02', 0, 1, 'character maps to <undefined>')
<tifffile.TiffTag 5033 @135616> coercing invalid ASCII to bytes, due to UnicodeDecodeError('charmap', b'\x8d', 0, 1, 'character maps to <undefined>')

---Image Registration---

translation = [ 3.771 -2.465]

rotation = -0.10616402004029624 

scale = 1.0005468557186985 


 registration difference vector: [np.float64(0.002000000000000224), np.float64(0.016000000000000014)]

<tifffile.TiffTag 5033 @135616> coercing invalid ASCII to bytes, due to UnicodeDecodeError('charmap', b'\x8d', 0, 1, 'character maps to <undefined>')
<tifffile.TiffTag 5031 @135592> coercing invalid ASCII to bytes, due to UnicodeDecodeError('charmap', b'\x81\n\x02', 0, 1, 'character maps to <undefined>')
<tifffile.TiffTag 5033 @135616> coercing invalid ASCII to bytes, due to UnicodeDecodeError('charmap', b'\x8d', 0, 1, 'character maps to <undefined>')

---Image Registration---

translation = [ 4.036 -2.502]

rotation = -0.1742128415235129 

scale = 0.998545513406686

difference_vectors = []
rdiffmag_scalers = []
for FoV in reg_dict_list_BMY823_20230725_1_C:
    rdiffmag_scalers.append(FoV['rdif_magnitude'])
    difference_vectors.append(FoV['diff_vec'])

rdiffmag_scalers = np.array(rdiffmag_scalers, dtype='float32')
difference_vectors = np.array(difference_vectors, dtype='float32')

rdiffmag_scalers

array([0.36087948, 0.01612451, 0.57913125, 0.8621444 , 0.4709533 ,
       0.7452684 , 0.10023971, 0.6555677 , 0.40362483, 0.6990851 ,
       0.06216912, 0.12264176, 0.86293745, 0.6816949 , 0.7629764 ,
       0.26075467, 0.81840944, 0.8215333 , 0.25695524, 0.08864536,
       0.13      , 0.4419423 , 0.761916  , 1.2047726 , 0.18811166,
       0.3402602 , 0.02816026, 0.05500909, 0.36778933, 0.8794322 ,
       0.19536889, 0.30291417, 0.21883784, 0.50992155, 1.0160639 ,
       0.21666795, 0.12709445, 0.24698178, 0.31396815, 0.6826434 ,
       0.6359819 , 0.19402319], dtype=float32)

np.std(rdiffmag_scalers)

np.float32(0.30733225)

std_diff_vector = np.std(np.array(difference_vectors), axis = 0)

std_diff_vector

array([0.40691665, 0.32704076], dtype=float32)

# math.sqrt(std_diff_vector[0]**2 + std_diff_vector[1]**2) is the non-numpy version
reg_prec_BMY823_20230725_1_C = np.sqrt(np.sum(np.square(std_diff_vector)))
reg_prec_BMY823_20230725_1_C

np.float32(0.52205056)

print(f"{2*reg_prec_BMY823_20230725_1_C} is 2sigma_reg.")

1.0441011190414429 is 2sigma_reg.

FoV_id_list = [FoV['FoV_id'] for FoV in reg_dict_list_BMY823_20230725_1_C]
is_outlier = rdiffmag_scalers > 2*reg_prec_BMY823_20230725_1_C

FoV_id_to_keep = [FoV for FoV, boolean_flag in zip(FoV_id_list, is_outlier) if not boolean_flag]
FoV_id_to_cull = [FoV for FoV, boolean_flag in zip(FoV_id_list, is_outlier) if boolean_flag]

for outlier in FoV_id_to_cull:
    print(f"FoV {outlier} has a registration difference with a magnitude greater than {2*reg_prec_BMY823_20230725_1_C} (2*reg_diff_prec)")

FoV 139 has a registration difference with a magnitude greater than 1.0441011190414429 (2*reg_diff_prec)

mRNA_tracking_data_list_dict = load_json_experiments_data("/home/jocelyn.tourtellotte-umw/yeast_json_output/tracking_experiments/")

Found 79 JSON files. Loading them...
 -> Loaded BMY820_BMY820_7_18_23_aqsettings1_batchB.json
 -> Loaded BMY820_BMY820_7_19_23_aqsettings1_batchA.json
 -> Loaded BMY820_BMY820_7_19_23_aqsettings1_batchB.json
 -> Loaded BMY820_BMY820_7_21_23_aqsettings1_batchA.json
 -> Loaded BMY820_BMY820_7_21_23_aqsettings1_batchC.json
 -> Loaded BMY820_BMY820_7_24_23_aqsettings1_batchA.json
 -> Loaded BMY820_BMY820_7_26_23_aqsettings1_batchA.json
 -> Loaded BMY820_BMY820_7_26_23_aqsettings1_batchB.json
 -> Loaded BMY820_BMY820_7_26_23_aqsettings1_batchC.json
 -> Loaded BMY820_BMY820_7_28_23_aqsettings1_batchB.json
 -> Loaded BMY820_BMY820_8_10_23_aqsettings1_batchA.json
 -> Loaded BMY820_BMY820_8_10_23_aqsettings1_batchB.json
 -> Loaded BMY820_BMY820_8_11_23_aqsettings1_batchA.json
 -> Loaded BMY820_BMY820_8_11_23_aqsettings1_batchB.json
 -> Loaded BMY820_BMY820_8_11_23_aqsettings1_batchC.json
 -> Loaded BMY820_BMY820_8_14_23_aqsettings1_batchA.json
 -> Loaded BMY820_BMY820_8_15_23_aqsettings1_batchA.json
 -> Loaded BMY820_BMY820_8_17_23_aqsettings1_batchD.json
 -> Loaded BMY820_BMY820_8_18_23_aqsettings1_batchC.json
 -> Loaded BMY820_BMY820_8_21_23_aqsettings1_batchA.json
 -> Loaded BMY820_BMY820_8_22_23_aqsettings1_batchD.json
 -> Loaded BMY820_BMY820_8_2_23_aqsettings1_batchA.json
 -> Loaded BMY820_BMY820_8_3_23_aqsettings1_batchC.json
 -> Loaded BMY820_BMY820_8_3_23_aqsettings1_batchD.json
 -> Loaded BMY820_BMY820_8_4_23_aqsettings1_batchC.json
 -> Loaded BMY820_BMY820_8_5_23_aqsettings1_batchD.json
 -> Loaded BMY820_BMY820_8_7_23_aqsettings1_batchA.json
 -> Loaded BMY820_BMY820_8_8_23_aqsettings1_batchB.json
 -> Loaded BMY820_BMY820_8_8_23_aqsettings1_batchC.json
 -> Loaded BMY822_BMY822_7_18_23_aqsettings1_batchA.json
 -> Loaded BMY822_BMY822_7_18_23_aqsettings1_batchD.json
 -> Loaded BMY822_BMY822_7_27_23_aqsettings1_batchA.json
 -> Loaded BMY822_BMY822_7_27_23_aqsettings1_batchB.json
 -> Loaded BMY822_BMY822_7_27_23_aqsettings1_batchC.json
 -> Loaded BMY822_BMY822_7_27_23_aqsettings1_batchD.json
 -> Loaded BMY822_BMY822_7_31_23_aqsettings1_batchA.json
 -> Loaded BMY822_BMY822_7_31_23_aqsettings1_batchB.json
 -> Loaded BMY822_BMY822_7_31_23_aqsettings1_batchC.json
 -> Loaded BMY822_BMY822_8_10_23_aqsettings1_batchC.json
 -> Loaded BMY822_BMY822_8_15_23_aqsettings1_batchD.json
 -> Loaded BMY822_BMY822_8_17_23_aqsettings1_batchA.json
 -> Loaded BMY822_BMY822_8_17_23_aqsettings1_batchC.json
 -> Loaded BMY822_BMY822_8_18_23_aqsettings1_batchB.json
 -> Loaded BMY822_BMY822_8_1_23_aqsettings1_batchA.json
 -> Loaded BMY822_BMY822_8_1_23_aqsettings1_batchB.json
 -> Loaded BMY822_BMY822_8_1_23_aqsettings1_batchC.json
 -> Loaded BMY822_BMY822_8_1_23_aqsettings1_batchD.json
 -> Loaded BMY822_BMY822_8_21_23_aqsettings1_batchB.json
 -> Loaded BMY822_BMY822_8_24_23_aqsettings1_batchB.json
 -> Loaded BMY822_BMY822_8_2_23_aqsettings1_batchC.json
 -> Loaded BMY822_BMY822_8_3_23_aqsettings1_batchA.json
 -> Loaded BMY822_BMY822_8_4_23_aqsettings1_batchA.json
 -> Loaded BMY822_BMY822_8_5_23_aqsettings1_batchD.json
 -> Loaded BMY822_BMY822_8_7_23_aqsettings1_batchB.json
 -> Loaded BMY822_BMY822_8_8_23_aqsettings1_batchA.json
 -> Loaded BMY822_BMY822_8_8_23_aqsettings1_batchD.json
 -> Loaded BMY823_BMY823_7_16_23_aqsettings1_batchA.json
 -> Loaded BMY823_BMY823_7_16_23_aqsettings1_batchB.json
 -> Loaded BMY823_BMY823_7_16_23_aqsettings1_batchC.json
 -> Loaded BMY823_BMY823_7_18_23_aqsettings1_batchD.json
 -> Loaded BMY823_BMY823_7_20_23_aqsettings1_batchA.json
 -> Loaded BMY823_BMY823_7_20_23_aqsettings1_batchB.json
 -> Loaded BMY823_BMY823_7_21_23_aqsettings1_batchB.json
 -> Loaded BMY823_BMY823_7_24_23_aqsettings1_batchB.json
 -> Loaded BMY823_BMY823_7_24_23_aqsettings1_batchC.json
 -> Loaded BMY823_BMY823_7_25_23_aqsettings1_batchA.json
 -> Loaded BMY823_BMY823_7_25_23_aqsettings1_batchB.json
 -> Loaded BMY823_BMY823_7_25_23_aqsettings1_batchC.json
 -> Loaded BMY823_BMY823_7_25_23_aqsettings1_batchD.json
 -> Loaded BMY823_BMY823_7_28_23_aqsettings1_batchA.json
 -> Loaded BMY823_BMY823_8_10_23_aqsettings1_batchD.json
 -> Loaded BMY823_BMY823_8_14_23_aqsettings1_batchB.json
 -> Loaded BMY823_BMY823_8_15_23_aqsettings1_batchB.json
 -> Loaded BMY823_BMY823_8_17_23_aqsettings1_batchB.json
 -> Loaded BMY823_BMY823_8_18_23_aqsettings1_batchA.json
 -> Loaded BMY823_BMY823_8_22_23_aqsettings1_batchB.json
 -> Loaded BMY823_BMY823_8_24_23_aqsettings1_batchA.json
 -> Loaded BMY823_BMY823_8_2_23_aqsettings1_batchB.json
 -> Loaded BMY823_BMY823_8_3_23_aqsettings1_batchB.json

all_exp_reg_dict_list = {}
for experiment_name in mRNA_tracking_data_list_dict: # for each experiment associated list of dictionaries
    print(experiment_name)
    current_reg_dict_list = []
    for FoV_dict in mRNA_tracking_data_list_dict[experiment_name]: # for each FoV dictionary in that list (dictionaries with paths to all affiliated FoV images)
        try:
            registration_result = image_registration(FoV_dict, False)
            current_reg_dict_list.append(registration_result) # calculate the registration difference etc
        except FileNotFoundError as e:
            print(f"    --> WARNING: File not found for FoV {FoV_dict.get('FoV_id', 'Unknown')}. Skipping. Error: {e}")
    output_path = f"/home/jocelyn.tourtellotte-umw/yeast_json_output/tracking_experiments/reg_result_{experiment_name}.json"
    with open(output_path, 'w') as f:
        json.dump(current_reg_dict_list, f, indent=4, cls=NumpyArrayEncoder)
        
    all_exp_reg_dict_list[experiment_name] = current_reg_dict_list

<tifffile.TiffTag 5033 @135616> coercing invalid ASCII to bytes, due to UnicodeDecodeError('charmap', b'\x8d', 0, 1, 'character maps to <undefined>')

BMY820_BMY820_7_18_23_aqsettings1_batchB

<tifffile.TiffTag 5031 @135592> coercing invalid ASCII to bytes, due to UnicodeDecodeError('charmap', b'\x81\n\x02', 0, 1, 'character maps to <undefined>')
<tifffile.TiffTag 5033 @135616> coercing invalid ASCII to bytes, due to UnicodeDecodeError('charmap', b'\x8d', 0, 1, 'character maps to <undefined>')
<tifffile.TiffTag 5033 @135616> coercing invalid ASCII to bytes, due to UnicodeDecodeError('charmap', b'\x8d', 0, 1, 'character maps to <undefined>')

---Image Registration---

translation = [ 3.992 -1.853]

rotation = -0.08710226865539994 

scale = 1.002642602624957

<tifffile.TiffTag 5031 @135592> coercing invalid ASCII to bytes, due to UnicodeDecodeError('charmap', b'\x81\n\x02', 0, 1, 'character maps to <undefined>')
<tifffile.TiffTag 5033 @135616> coercing invalid ASCII to bytes, due to UnicodeDecodeError('charmap', b'\x8d', 0, 1, 'character maps to <undefined>')
<tifffile.TiffTag 5033 @135616> coercing invalid ASCII to bytes, due to UnicodeDecodeError('charmap', b'\x8d', 0, 1, 'character maps to <undefined>')

---Image Registration---

translation = [ 3.509 -2.334]

rotation = -0.12343094725329706 

scale = 1.0016988074678455 


 registration difference vector: [np.float64(0.4830000000000001), np.float64(0.4810000000000001)]

<tifffile.TiffTag 5031 @135592> coercing invalid ASCII to bytes, due to UnicodeDecodeError('charmap', b'\x81\n\x02', 0, 1, 'character maps to <undefined>')
<tifffile.TiffTag 5033 @135616> coercing invalid ASCII to bytes, due to UnicodeDecodeError('charmap', b'\x8d', 0, 1, 'character maps to <undefined>')
<tifffile.TiffTag 5033 @135616> coercing invalid ASCII to bytes, due to UnicodeDecodeError('charmap', b'\x8d', 0, 1, 'character maps to <undefined>')

---Image Registration---

translation = [ 3.871 -1.814]

rotation = -0.12156266682762862 

scale = 1.000987867554169

<tifffile.TiffTag 5031 @135592> coercing invalid ASCII to bytes, due to UnicodeDecodeError('charmap', b'\x81\n\x02', 0, 1, 'character maps to <undefined>')
<tifffile.TiffTag 5033 @135616> coercing invalid ASCII to bytes, due to UnicodeDecodeError('charmap', b'\x8d', 0, 1, 'character maps to <undefined>')
<tifffile.TiffTag 5033 @135616> coercing invalid ASCII to bytes, due to UnicodeDecodeError('charmap', b'\x8d', 0, 1, 'character maps to <undefined>')

---Image Registration---

translation = [ 3.769 -2.462]

rotation = -0.1327571464846642 

scale = 1.0017037474711834 


 registration difference vector: [np.float64(0.10199999999999987), np.float64(0.6480000000000001)]

for experiment_name in all_exp_reg_dict_list:
    print(experiment_name)

BMY820_BMY820_7_18_23_aqsettings1_batchB
BMY820_BMY820_7_19_23_aqsettings1_batchA
BMY820_BMY820_7_19_23_aqsettings1_batchB
BMY820_BMY820_7_21_23_aqsettings1_batchA
BMY820_BMY820_7_21_23_aqsettings1_batchC
BMY820_BMY820_7_24_23_aqsettings1_batchA
BMY820_BMY820_7_26_23_aqsettings1_batchA
BMY820_BMY820_7_26_23_aqsettings1_batchB
BMY820_BMY820_7_26_23_aqsettings1_batchC
BMY820_BMY820_7_28_23_aqsettings1_batchB
BMY820_BMY820_8_10_23_aqsettings1_batchA
BMY820_BMY820_8_10_23_aqsettings1_batchB
BMY820_BMY820_8_11_23_aqsettings1_batchA
BMY820_BMY820_8_11_23_aqsettings1_batchB
BMY820_BMY820_8_11_23_aqsettings1_batchC
BMY820_BMY820_8_14_23_aqsettings1_batchA
BMY820_BMY820_8_15_23_aqsettings1_batchA
BMY820_BMY820_8_17_23_aqsettings1_batchD
BMY820_BMY820_8_18_23_aqsettings1_batchC
BMY820_BMY820_8_21_23_aqsettings1_batchA
BMY820_BMY820_8_22_23_aqsettings1_batchD
BMY820_BMY820_8_2_23_aqsettings1_batchA
BMY820_BMY820_8_3_23_aqsettings1_batchC
BMY820_BMY820_8_3_23_aqsettings1_batchD
BMY820_BMY820_8_4_23_aqsettings1_batchC
BMY820_BMY820_8_5_23_aqsettings1_batchD
BMY820_BMY820_8_7_23_aqsettings1_batchA
BMY820_BMY820_8_8_23_aqsettings1_batchB
BMY820_BMY820_8_8_23_aqsettings1_batchC
BMY822_BMY822_7_18_23_aqsettings1_batchA
BMY822_BMY822_7_18_23_aqsettings1_batchD
BMY822_BMY822_7_27_23_aqsettings1_batchA
BMY822_BMY822_7_27_23_aqsettings1_batchB
BMY822_BMY822_7_27_23_aqsettings1_batchC
BMY822_BMY822_7_27_23_aqsettings1_batchD
BMY822_BMY822_7_31_23_aqsettings1_batchA
BMY822_BMY822_7_31_23_aqsettings1_batchB
BMY822_BMY822_7_31_23_aqsettings1_batchC
BMY822_BMY822_8_10_23_aqsettings1_batchC
BMY822_BMY822_8_15_23_aqsettings1_batchD
BMY822_BMY822_8_17_23_aqsettings1_batchA
BMY822_BMY822_8_17_23_aqsettings1_batchC
BMY822_BMY822_8_18_23_aqsettings1_batchB
BMY822_BMY822_8_1_23_aqsettings1_batchA
BMY822_BMY822_8_1_23_aqsettings1_batchB
BMY822_BMY822_8_1_23_aqsettings1_batchC
BMY822_BMY822_8_1_23_aqsettings1_batchD
BMY822_BMY822_8_21_23_aqsettings1_batchB
BMY822_BMY822_8_24_23_aqsettings1_batchB
BMY822_BMY822_8_2_23_aqsettings1_batchC
BMY822_BMY822_8_3_23_aqsettings1_batchA
BMY822_BMY822_8_4_23_aqsettings1_batchA
BMY822_BMY822_8_5_23_aqsettings1_batchD
BMY822_BMY822_8_7_23_aqsettings1_batchB
BMY822_BMY822_8_8_23_aqsettings1_batchA
BMY822_BMY822_8_8_23_aqsettings1_batchD
BMY823_BMY823_7_16_23_aqsettings1_batchA
BMY823_BMY823_7_16_23_aqsettings1_batchB
BMY823_BMY823_7_16_23_aqsettings1_batchC
BMY823_BMY823_7_18_23_aqsettings1_batchD
BMY823_BMY823_7_20_23_aqsettings1_batchA
BMY823_BMY823_7_20_23_aqsettings1_batchB
BMY823_BMY823_7_21_23_aqsettings1_batchB
BMY823_BMY823_7_24_23_aqsettings1_batchB
BMY823_BMY823_7_24_23_aqsettings1_batchC
BMY823_BMY823_7_25_23_aqsettings1_batchA
BMY823_BMY823_7_25_23_aqsettings1_batchB
BMY823_BMY823_7_25_23_aqsettings1_batchC
BMY823_BMY823_7_25_23_aqsettings1_batchD
BMY823_BMY823_7_28_23_aqsettings1_batchA
BMY823_BMY823_8_10_23_aqsettings1_batchD
BMY823_BMY823_8_14_23_aqsettings1_batchB
BMY823_BMY823_8_15_23_aqsettings1_batchB
BMY823_BMY823_8_17_23_aqsettings1_batchB
BMY823_BMY823_8_18_23_aqsettings1_batchA
BMY823_BMY823_8_22_23_aqsettings1_batchB
BMY823_BMY823_8_24_23_aqsettings1_batchA
BMY823_BMY823_8_2_23_aqsettings1_batchB
BMY823_BMY823_8_3_23_aqsettings1_batchB

reg_results_by_experiment = []
for experiment_name in all_exp_reg_dict_list: # for each experiment associated list of dictionaries
    print(experiment_name)
    # is a set of image registration results
    std_diff_vector, reg_prec, FoV_to_retain, is_outlier = check_reg_prec(all_exp_reg_dict_list[experiment_name])
    reg_results_by_experiment.append({'experiment_name':experiment_name,
                                      'std_diff_vector': std_diff_vector,
                                      'reg_precision_mag': reg_prec,
                                      'FoV_to_retain':FoV_to_retain,
                                      'FoV_to_drop': is_outlier})
    print(f"reg-diff sigma vector: {std_diff_vector}")
    print(f"reg-diff precision: {reg_prec}")
    print(f"FoV reg-diff less than 2sigma {len(FoV_to_retain)} of {len(is_outlier) + len(FoV_to_retain)}")
    print(f"or {len(FoV_to_retain) / (len(is_outlier) + len(FoV_to_retain))}")
    
# reg_results_by_experiment

BMY820_BMY820_7_18_23_aqsettings1_batchB
0.9308140873908997 is 2sigma_reg.
reg-diff sigma vector: [0.35103634 0.30557683]
reg-diff precision: 0.46540704369544983
FoV reg-diff less than 2sigma 34 of 68
or 0.5
BMY820_BMY820_7_19_23_aqsettings1_batchA
1.1120942831039429 is 2sigma_reg.
reg-diff sigma vector: [0.44967616 0.3270776 ]
reg-diff precision: 0.5560471415519714
FoV reg-diff less than 2sigma 62 of 126
or 0.49206349206349204
BMY820_BMY820_7_19_23_aqsettings1_batchB
0.9549047350883484 is 2sigma_reg.
reg-diff sigma vector: [0.4104226 0.243955 ]
reg-diff precision: 0.4774523675441742
FoV reg-diff less than 2sigma 70 of 141
or 0.49645390070921985
BMY820_BMY820_7_21_23_aqsettings1_batchA
1.1156747341156006 is 2sigma_reg.
reg-diff sigma vector: [0.45607066 0.3212197 ]
reg-diff precision: 0.5578373670578003
FoV reg-diff less than 2sigma 41 of 82
or 0.5
BMY820_BMY820_7_21_23_aqsettings1_batchC
16.34886360168457 is 2sigma_reg.
reg-diff sigma vector: [6.840798  4.4749103]
reg-diff precision: 8.174431800842285
FoV reg-diff less than 2sigma 31 of 64
or 0.484375
BMY820_BMY820_7_24_23_aqsettings1_batchA
1.1037354469299316 is 2sigma_reg.
reg-diff sigma vector: [0.37685266 0.4031626 ]
reg-diff precision: 0.5518677234649658
FoV reg-diff less than 2sigma 67 of 137
or 0.48905109489051096
BMY820_BMY820_7_26_23_aqsettings1_batchA
1.131391167640686 is 2sigma_reg.
reg-diff sigma vector: [0.43375826 0.36313254]
reg-diff precision: 0.565695583820343
FoV reg-diff less than 2sigma 41 of 84
or 0.4880952380952381
BMY820_BMY820_7_26_23_aqsettings1_batchB
1.0652422904968262 is 2sigma_reg.
reg-diff sigma vector: [0.40248543 0.34884202]
reg-diff precision: 0.5326211452484131
FoV reg-diff less than 2sigma 58 of 118
or 0.4915254237288136
BMY820_BMY820_7_26_23_aqsettings1_batchC
0.9888957738876343 is 2sigma_reg.
reg-diff sigma vector: [0.35730946 0.3417728 ]
reg-diff precision: 0.49444788694381714
FoV reg-diff less than 2sigma 34 of 69
or 0.4927536231884058
BMY820_BMY820_7_28_23_aqsettings1_batchB
0.7816164493560791 is 2sigma_reg.
reg-diff sigma vector: [0.29409793 0.25736642]
reg-diff precision: 0.39080822467803955
FoV reg-diff less than 2sigma 52 of 107
or 0.48598130841121495
BMY820_BMY820_8_10_23_aqsettings1_batchA
1.0582343339920044 is 2sigma_reg.
reg-diff sigma vector: [0.31304583 0.42657623]
reg-diff precision: 0.5291171669960022
FoV reg-diff less than 2sigma 46 of 92
or 0.5
BMY820_BMY820_8_10_23_aqsettings1_batchB
0.818825364112854 is 2sigma_reg.
reg-diff sigma vector: [0.28096327 0.29778916]
reg-diff precision: 0.409412682056427
FoV reg-diff less than 2sigma 27 of 55
or 0.4909090909090909
BMY820_BMY820_8_11_23_aqsettings1_batchA
0.7687684893608093 is 2sigma_reg.
reg-diff sigma vector: [0.3655 0.119 ]
reg-diff precision: 0.38438424468040466
FoV reg-diff less than 2sigma 1 of 3
or 0.3333333333333333
BMY820_BMY820_8_11_23_aqsettings1_batchB
0.7769905924797058 is 2sigma_reg.
reg-diff sigma vector: [0.28126058 0.26799452]
reg-diff precision: 0.3884952962398529
FoV reg-diff less than 2sigma 23 of 50
or 0.46
BMY820_BMY820_8_11_23_aqsettings1_batchC
1.0209022760391235 is 2sigma_reg.
reg-diff sigma vector: [0.37963653 0.34122795]
reg-diff precision: 0.5104511380195618
FoV reg-diff less than 2sigma 38 of 78
or 0.48717948717948717
BMY820_BMY820_8_14_23_aqsettings1_batchA
0.9565739631652832 is 2sigma_reg.
reg-diff sigma vector: [0.3080899  0.36584017]
reg-diff precision: 0.4782869815826416
FoV reg-diff less than 2sigma 56 of 112
or 0.5
BMY820_BMY820_8_15_23_aqsettings1_batchA
0.9120954275131226 is 2sigma_reg.
reg-diff sigma vector: [0.29383618 0.34876904]
reg-diff precision: 0.4560477137565613
FoV reg-diff less than 2sigma 50 of 101
or 0.49504950495049505
BMY820_BMY820_8_17_23_aqsettings1_batchD
0.8275630474090576 is 2sigma_reg.
reg-diff sigma vector: [0.25933385 0.32242998]
reg-diff precision: 0.4137815237045288
FoV reg-diff less than 2sigma 9 of 19
or 0.47368421052631576
BMY820_BMY820_8_18_23_aqsettings1_batchC
0.7529022693634033 is 2sigma_reg.
reg-diff sigma vector: [0.2140644  0.30966416]
reg-diff precision: 0.37645113468170166
FoV reg-diff less than 2sigma 21 of 43
or 0.4883720930232558
BMY820_BMY820_8_21_23_aqsettings1_batchA
72.50416564941406 is 2sigma_reg.
reg-diff sigma vector: [20.729198 29.740778]
reg-diff precision: 36.25208282470703
FoV reg-diff less than 2sigma 17 of 35
or 0.4857142857142857
BMY820_BMY820_8_22_23_aqsettings1_batchD
0.7217513918876648 is 2sigma_reg.
reg-diff sigma vector: [0.28439817 0.22214624]
reg-diff precision: 0.3608756959438324
FoV reg-diff less than 2sigma 9 of 20
or 0.45
BMY820_BMY820_8_2_23_aqsettings1_batchA
1.4040858745574951 is 2sigma_reg.
reg-diff sigma vector: [0.36387658 0.6003817 ]
reg-diff precision: 0.7020429372787476
FoV reg-diff less than 2sigma 41 of 83
or 0.4939759036144578
BMY820_BMY820_8_3_23_aqsettings1_batchC
0.8123996257781982 is 2sigma_reg.
reg-diff sigma vector: [0.22910835 0.33542162]
reg-diff precision: 0.4061998128890991
FoV reg-diff less than 2sigma 47 of 94
or 0.5
BMY820_BMY820_8_3_23_aqsettings1_batchD
86.82537078857422 is 2sigma_reg.
reg-diff sigma vector: [26.609966 34.30118 ]
reg-diff precision: 43.41268539428711
FoV reg-diff less than 2sigma 13 of 27
or 0.48148148148148145
BMY820_BMY820_8_4_23_aqsettings1_batchC
0.8790973424911499 is 2sigma_reg.
reg-diff sigma vector: [0.26874608 0.34781978]
reg-diff precision: 0.43954867124557495
FoV reg-diff less than 2sigma 30 of 60
or 0.5
BMY820_BMY820_8_5_23_aqsettings1_batchD
0.6588770747184753 is 2sigma_reg.
reg-diff sigma vector: [0.22725917 0.23850161]
reg-diff precision: 0.32943853735923767
FoV reg-diff less than 2sigma 17 of 35
or 0.4857142857142857
BMY820_BMY820_8_7_23_aqsettings1_batchA
0.817418098449707 is 2sigma_reg.
reg-diff sigma vector: [0.25135836 0.32227638]
reg-diff precision: 0.4087090492248535
FoV reg-diff less than 2sigma 26 of 54
or 0.48148148148148145
BMY820_BMY820_8_8_23_aqsettings1_batchB
1.3164435625076294 is 2sigma_reg.
reg-diff sigma vector: [0.46031535 0.47049516]
reg-diff precision: 0.6582217812538147
FoV reg-diff less than 2sigma 4 of 8
or 0.5
BMY820_BMY820_8_8_23_aqsettings1_batchC
0.7630841135978699 is 2sigma_reg.
reg-diff sigma vector: [0.20912656 0.31912446]
reg-diff precision: 0.38154205679893494
FoV reg-diff less than 2sigma 26 of 52
or 0.5
BMY822_BMY822_7_18_23_aqsettings1_batchA
1.0125908851623535 is 2sigma_reg.
reg-diff sigma vector: [0.38065615 0.33382028]
reg-diff precision: 0.5062954425811768
FoV reg-diff less than 2sigma 72 of 146
or 0.4931506849315068
BMY822_BMY822_7_18_23_aqsettings1_batchD
0.9557501077651978 is 2sigma_reg.
reg-diff sigma vector: [0.3091073  0.36444098]
reg-diff precision: 0.4778750538825989
FoV reg-diff less than 2sigma 12 of 24
or 0.5
BMY822_BMY822_7_27_23_aqsettings1_batchA
1.0800334215164185 is 2sigma_reg.
reg-diff sigma vector: [0.41765803 0.34231535]
reg-diff precision: 0.5400167107582092
FoV reg-diff less than 2sigma 68 of 138
or 0.4927536231884058
BMY822_BMY822_7_27_23_aqsettings1_batchB
1.0320993661880493 is 2sigma_reg.
reg-diff sigma vector: [0.36580783 0.36399442]
reg-diff precision: 0.5160496830940247
FoV reg-diff less than 2sigma 37 of 75
or 0.49333333333333335
BMY822_BMY822_7_27_23_aqsettings1_batchC
0.8927305936813354 is 2sigma_reg.
reg-diff sigma vector: [0.32371524 0.30732787]
reg-diff precision: 0.4463652968406677
FoV reg-diff less than 2sigma 30 of 63
or 0.47619047619047616
BMY822_BMY822_7_27_23_aqsettings1_batchD
0.9972984194755554 is 2sigma_reg.
reg-diff sigma vector: [0.372317   0.33170936]
reg-diff precision: 0.4986492097377777
FoV reg-diff less than 2sigma 14 of 28
or 0.5
BMY822_BMY822_7_31_23_aqsettings1_batchA
0.9425799250602722 is 2sigma_reg.
reg-diff sigma vector: [0.27264598 0.38441956]
reg-diff precision: 0.4712899625301361
FoV reg-diff less than 2sigma 44 of 92
or 0.4782608695652174
BMY822_BMY822_7_31_23_aqsettings1_batchB
0.8701836466789246 is 2sigma_reg.
reg-diff sigma vector: [0.2936758  0.32102868]
reg-diff precision: 0.4350918233394623
FoV reg-diff less than 2sigma 29 of 58
or 0.5
BMY822_BMY822_7_31_23_aqsettings1_batchC
0.19901129603385925 is 2sigma_reg.
reg-diff sigma vector: [0.08085597 0.0579973 ]
reg-diff precision: 0.09950564801692963
FoV reg-diff less than 2sigma 0 of 4
or 0.0
BMY822_BMY822_8_10_23_aqsettings1_batchC
0.942717969417572 is 2sigma_reg.
reg-diff sigma vector: [0.3295017  0.33705774]
reg-diff precision: 0.471358984708786
FoV reg-diff less than 2sigma 55 of 113
or 0.48672566371681414
BMY822_BMY822_8_15_23_aqsettings1_batchD
0.9559751749038696 is 2sigma_reg.
reg-diff sigma vector: [0.31207192 0.3620542 ]
reg-diff precision: 0.4779875874519348
FoV reg-diff less than 2sigma 45 of 90
or 0.5
BMY822_BMY822_8_17_23_aqsettings1_batchA
3.367337703704834 is 2sigma_reg.
reg-diff sigma vector: [0.439475  1.6253006]
reg-diff precision: 1.683668851852417
FoV reg-diff less than 2sigma 32 of 65
or 0.49230769230769234
BMY822_BMY822_8_17_23_aqsettings1_batchC
0.9835394620895386 is 2sigma_reg.
reg-diff sigma vector: [0.35391796 0.34143746]
reg-diff precision: 0.4917697310447693
FoV reg-diff less than 2sigma 21 of 42
or 0.5
BMY822_BMY822_8_18_23_aqsettings1_batchB
0.9699384570121765 is 2sigma_reg.
reg-diff sigma vector: [0.35822338 0.32691157]
reg-diff precision: 0.48496922850608826
FoV reg-diff less than 2sigma 15 of 30
or 0.5
BMY822_BMY822_8_1_23_aqsettings1_batchA
0.9209917187690735 is 2sigma_reg.
reg-diff sigma vector: [0.31983113 0.3313072 ]
reg-diff precision: 0.46049585938453674
FoV reg-diff less than 2sigma 54 of 109
or 0.4954128440366973
BMY822_BMY822_8_1_23_aqsettings1_batchB
7.871850967407227 is 2sigma_reg.
reg-diff sigma vector: [3.9113278  0.43934375]
reg-diff precision: 3.9359254837036133
FoV reg-diff less than 2sigma 34 of 69
or 0.4927536231884058
BMY822_BMY822_8_1_23_aqsettings1_batchC
1.204811930656433 is 2sigma_reg.
reg-diff sigma vector: [0.38962418 0.45944092]
reg-diff precision: 0.6024059653282166
FoV reg-diff less than 2sigma 41 of 83
or 0.4939759036144578
BMY822_BMY822_8_1_23_aqsettings1_batchD
1.8734639883041382 is 2sigma_reg.
reg-diff sigma vector: [0.78222084 0.5153614 ]
reg-diff precision: 0.9367319941520691
FoV reg-diff less than 2sigma 44 of 89
or 0.4943820224719101
BMY822_BMY822_8_21_23_aqsettings1_batchB
57.07061004638672 is 2sigma_reg.
reg-diff sigma vector: [28.294317   3.7007115]
reg-diff precision: 28.53530502319336
FoV reg-diff less than 2sigma 17 of 35
or 0.4857142857142857
BMY822_BMY822_8_24_23_aqsettings1_batchB
0.9987509846687317 is 2sigma_reg.
reg-diff sigma vector: [0.37340552 0.33157834]
reg-diff precision: 0.49937549233436584
FoV reg-diff less than 2sigma 21 of 42
or 0.5
BMY822_BMY822_8_2_23_aqsettings1_batchC
1.124624252319336 is 2sigma_reg.
reg-diff sigma vector: [0.41695148 0.37728825]
reg-diff precision: 0.562312126159668
FoV reg-diff less than 2sigma 21 of 43
or 0.4883720930232558
BMY822_BMY822_8_3_23_aqsettings1_batchA
18.468992233276367 is 2sigma_reg.
reg-diff sigma vector: [8.825276  2.7185314]
reg-diff precision: 9.234496116638184
FoV reg-diff less than 2sigma 40 of 82
or 0.4878048780487805
BMY822_BMY822_8_4_23_aqsettings1_batchA
0.964243471622467 is 2sigma_reg.
reg-diff sigma vector: [0.3140275  0.36582527]
reg-diff precision: 0.4821217358112335
FoV reg-diff less than 2sigma 62 of 125
or 0.496
BMY822_BMY822_8_5_23_aqsettings1_batchD
0.5570968985557556 is 2sigma_reg.
reg-diff sigma vector: [0.213  0.1795]
reg-diff precision: 0.2785484492778778
FoV reg-diff less than 2sigma 1 of 3
or 0.3333333333333333
BMY822_BMY822_8_7_23_aqsettings1_batchB
1.021939754486084 is 2sigma_reg.
reg-diff sigma vector: [0.33323258 0.387358  ]
reg-diff precision: 0.510969877243042
FoV reg-diff less than 2sigma 36 of 72
or 0.5
BMY822_BMY822_8_8_23_aqsettings1_batchA
0.999234139919281 is 2sigma_reg.
reg-diff sigma vector: [0.32697746 0.37776044]
reg-diff precision: 0.4996170699596405
FoV reg-diff less than 2sigma 55 of 110
or 0.5
BMY822_BMY822_8_8_23_aqsettings1_batchD
0.8558268547058105 is 2sigma_reg.
reg-diff sigma vector: [0.30087623 0.3042752 ]
reg-diff precision: 0.4279134273529053
FoV reg-diff less than 2sigma 63 of 130
or 0.4846153846153846
BMY823_BMY823_7_16_23_aqsettings1_batchA
1.3486758470535278 is 2sigma_reg.
reg-diff sigma vector: [0.39441904 0.54696   ]
reg-diff precision: 0.6743379235267639
FoV reg-diff less than 2sigma 33 of 68
or 0.4852941176470588
BMY823_BMY823_7_16_23_aqsettings1_batchB
38.7880973815918 is 2sigma_reg.
reg-diff sigma vector: [17.264755  8.835004]
reg-diff precision: 19.3940486907959
FoV reg-diff less than 2sigma 30 of 61
or 0.4918032786885246
BMY823_BMY823_7_16_23_aqsettings1_batchC
1.0002974271774292 is 2sigma_reg.
reg-diff sigma vector: [0.41842335 0.2739902 ]
reg-diff precision: 0.5001487135887146
FoV reg-diff less than 2sigma 54 of 108
or 0.5
BMY823_BMY823_7_18_23_aqsettings1_batchD
0.762912392616272 is 2sigma_reg.
reg-diff sigma vector: [0.28566763 0.25279012]
reg-diff precision: 0.381456196308136
FoV reg-diff less than 2sigma 9 of 18
or 0.5
BMY823_BMY823_7_20_23_aqsettings1_batchA
0.9121821522712708 is 2sigma_reg.
reg-diff sigma vector: [0.36511266 0.27333462]
reg-diff precision: 0.4560910761356354
FoV reg-diff less than 2sigma 49 of 100
or 0.49
BMY823_BMY823_7_20_23_aqsettings1_batchB
1.043259620666504 is 2sigma_reg.
reg-diff sigma vector: [0.43018615 0.29502127]
reg-diff precision: 0.521629810333252
FoV reg-diff less than 2sigma 59 of 121
or 0.48760330578512395
BMY823_BMY823_7_21_23_aqsettings1_batchB
1.0378994941711426 is 2sigma_reg.
reg-diff sigma vector: [0.37246698 0.36135468]
reg-diff precision: 0.5189497470855713
FoV reg-diff less than 2sigma 48 of 97
or 0.4948453608247423
BMY823_BMY823_7_24_23_aqsettings1_batchB
0.8805726170539856 is 2sigma_reg.
reg-diff sigma vector: [0.33765915 0.2825568 ]
reg-diff precision: 0.4402863085269928
FoV reg-diff less than 2sigma 60 of 120
or 0.5
BMY823_BMY823_7_24_23_aqsettings1_batchC
0.9612656831741333 is 2sigma_reg.
reg-diff sigma vector: [0.3895335 0.2815521]
reg-diff precision: 0.48063284158706665
FoV reg-diff less than 2sigma 68 of 138
or 0.4927536231884058
BMY823_BMY823_7_25_23_aqsettings1_batchA
20.375314712524414 is 2sigma_reg.
reg-diff sigma vector: [5.038867 8.854275]
reg-diff precision: 10.187657356262207
FoV reg-diff less than 2sigma 80 of 162
or 0.49382716049382713
BMY823_BMY823_7_25_23_aqsettings1_batchB
0.9585821628570557 is 2sigma_reg.
reg-diff sigma vector: [0.3499327  0.32751647]
reg-diff precision: 0.47929108142852783
FoV reg-diff less than 2sigma 27 of 55
or 0.4909090909090909
BMY823_BMY823_7_25_23_aqsettings1_batchC
1.0441011190414429 is 2sigma_reg.
reg-diff sigma vector: [0.40691665 0.32704076]
reg-diff precision: 0.5220505595207214
FoV reg-diff less than 2sigma 41 of 83
or 0.4939759036144578
BMY823_BMY823_7_25_23_aqsettings1_batchD
7.5364203453063965 is 2sigma_reg.
reg-diff sigma vector: [2.8524933 2.462253 ]
reg-diff precision: 3.7682101726531982
FoV reg-diff less than 2sigma 26 of 53
or 0.49056603773584906
BMY823_BMY823_7_28_23_aqsettings1_batchA
1.2045751810073853 is 2sigma_reg.
reg-diff sigma vector: [0.45441774 0.39529085]
reg-diff precision: 0.6022875905036926
FoV reg-diff less than 2sigma 66 of 132
or 0.5
BMY823_BMY823_8_10_23_aqsettings1_batchD
0.9430573582649231 is 2sigma_reg.
reg-diff sigma vector: [0.31070757 0.3546831 ]
reg-diff precision: 0.47152867913246155
FoV reg-diff less than 2sigma 66 of 133
or 0.49624060150375937
BMY823_BMY823_8_14_23_aqsettings1_batchB
0.8984357118606567 is 2sigma_reg.
reg-diff sigma vector: [0.24172005 0.3786398 ]
reg-diff precision: 0.44921785593032837
FoV reg-diff less than 2sigma 43 of 86
or 0.5
BMY823_BMY823_8_15_23_aqsettings1_batchB
1.1367863416671753 is 2sigma_reg.
reg-diff sigma vector: [0.43878287 0.36130372]
reg-diff precision: 0.5683931708335876
FoV reg-diff less than 2sigma 35 of 71
or 0.49295774647887325
BMY823_BMY823_8_17_23_aqsettings1_batchB
1.0132094621658325 is 2sigma_reg.
reg-diff sigma vector: [0.27661029 0.42442328]
reg-diff precision: 0.5066047310829163
FoV reg-diff less than 2sigma 36 of 72
or 0.5
BMY823_BMY823_8_18_23_aqsettings1_batchA
0.9147782921791077 is 2sigma_reg.
reg-diff sigma vector: [0.28964186 0.35399497]
reg-diff precision: 0.45738914608955383
FoV reg-diff less than 2sigma 41 of 82
or 0.5
BMY823_BMY823_8_22_23_aqsettings1_batchB
1.0962846279144287 is 2sigma_reg.
reg-diff sigma vector: [0.33775264 0.43172115]
reg-diff precision: 0.5481423139572144
FoV reg-diff less than 2sigma 25 of 51
or 0.49019607843137253
BMY823_BMY823_8_24_23_aqsettings1_batchA
1.1734535694122314 is 2sigma_reg.
reg-diff sigma vector: [0.3323564  0.48351583]
reg-diff precision: 0.5867267847061157
FoV reg-diff less than 2sigma 26 of 53
or 0.49056603773584906
BMY823_BMY823_8_2_23_aqsettings1_batchB
1.1467764377593994 is 2sigma_reg.
reg-diff sigma vector: [0.39846072 0.41231433]
reg-diff precision: 0.5733882188796997
FoV reg-diff less than 2sigma 29 of 60
or 0.48333333333333334
BMY823_BMY823_8_3_23_aqsettings1_batchB
1.3143646717071533 is 2sigma_reg.
reg-diff sigma vector: [0.4304186  0.49661702]
reg-diff precision: 0.6571823358535767
FoV reg-diff less than 2sigma 27 of 54
or 0.5

output_path = "/home/jocelyn.tourtellotte-umw/yeast_json_output/tracking_experiments/reg_results_summary.json"
with open(output_path, 'w') as f:
    json.dump(reg_results_by_experiment, f, indent=4, cls=NumpyArrayEncoder)

print(f"Successfully saved results to {output_path}")

Successfully saved results to /home/jocelyn.tourtellotte-umw/yeast_json_output/tracking_experiments/reg_results_summary.json

Example Batch¶

Running across multiple experiments within a main directory¶